I'm saying that in context of market realities, the other browsers won't use shared Google-source as the "implementation is the specification" for NaCl/Pepper, and no one can write a real NaCl/Pepper spec by which any browser could implement an independent and interoperable workalike in less than decades.
So why try if the OSes can do their own non-interoperating workalikes? (And they are already doing this, from what I hear.) If safe native code on the web is mainly for plugins, there's no problem. Plugins are OS-specific today and likely to remain so, safety or no.
Moving the Web VM to a more abstract level... hmm, sounds like JS as better compiler target over time. See also https://github.com/kripken/emscripten/.